Analysis of RNA-seq data from nasal cultures

SS Satria P. Sajuthi
PD Peter DeFord
YL Yingchun Li
NJ Nathan D. Jackson
MM Michael T. Montgomery
JE Jamie L. Everman
CR Cydney L. Rios
EP Elmar Pruesse
JN James D. Nolin
EP Elizabeth G. Plender
MW Michael E. Wechsler
AM Angel C. Y. Mak
CE Celeste Eng
SS Sandra Salazar
VM Vivian Medina
EW Eric M. Wohlford
SH Scott Huntsman
DN Deborah A. Nickerson
SG Soren Germer
MZ Michael C. Zody
GA Gonçalo Abecasis
HK Hyun Min Kang
KR Kenneth M. Rice
RK Rajesh Kumar
SO Sam Oh
JR Jose Rodriguez-Santana
EB Esteban G. Burchard
MS Max A. Seibold
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Raw sequencing reads were trimmed using a skewer with the following parameter settings: end-quality=15, mean-quality=25, min=30. Trimmed reads were then aligned to the human reference genome GRCh38 using HISAT281 (v2.1.0) using default parameter settings. Gene quantification was performed with htseq-count using the GRCh38 Ensembl v84 gene transcript model. After removing mitochondrial, ribosomal, and lowly expressed genes (those not expressed in at least two samples), we carried out differential expression analyses between paired IL-13-stimulated and control samples (n = 5 donors) and between paired HRV-infected and control samples (n = 5 donors) using the DESeq2 R package (v1.22.2).

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